Noble Mission emulated his legendary elder brother Frankel by winning the Champion Stakes after a thrilling duel with runner-up Al Kazeem.
The 7-1 shot, ridden by James Doyle for trainer Lady Cecil, won by a neck from Al Kazeem with Free Eagle in third.
Doyle was later given a seven-day ban and £10,000 fine for whip overuse.
Frankel's final victory came two years ago in this mile-and-a-quarter contest, the feature race on Champions Day, the richest raceday in Britain.
Noble Mission led from the front and dug in to secure an emotional triumph.
Lady Cecil took over Noble Mission's training licence after the death last summer of her husband, 10-time champion trainer Sir Henry Cecil who oversaw Frankel's unbeaten 14-race career.
"James gave him a great ride as he (Noble Mission) really had to dig deep," said Lady Cecil. "He's just enjoying it so much these days - he loves his racing.
"It's a great team effort, I'm so lucky."
Teddy Grimthorpe, racing manager for Noble Mission's owner, Khalid Abdullah, added: "It's a fairytale, it really is."
While romantics may have hoped Frankel's younger brother might be good enough to also win the race, it was the French-trained Cirrus Des Aigles who was sent off favourite.
Cirrus Des Aigles won the 2011 Champion Stakes and was runner-up in the next two runnings to Frankel and Farrh, but was out of the places on this occasion.
A stewards inquiry cautioned Doyle about his future conduct, finding him "guilty of careless riding" in the final furlong by taking second-placed Al Kazeem "marginally off his intended line".
Doyle said: "I'm not fuming - there are rules and at the end of the day you have to abide within them, but it is frustrating.
"In the heat of the battle, it is hard to keep count, and I didn't realise I'd gone over. I'll have a look at an appeal but I think it's unlikely."
Earlier, Forgotten Rules triumphed in the Long Distance Cup as The Queen's horse Estimate finished last in her final race.
|Cornelius Lysaght, BBC racing correspondent|
|I think that was as good a race as I've seen all season. Not only was it a thrilling, nostril-to-nostril encounter between two horses at the top of their games, but the result presented us with all the kind of emotion and poignancy that sport in general, but racing in particular, is so good at serving up. It's incalculable how much this has done for Jane Cecil. Following the legend that was Sir Henry was hard enough in those circumstances, and plenty shook their heads saying she'd never succeed. She certainly did here.|
The 3-1 winner, ridden by Pat Smullen for Irish trainer Dermot Weld, triumphed by a length and three quarters in only his third career start.
Biographer (25-1) was second, with 8-1 chance Pallasator in third, while favourite Leading Light came seventh after the winner swerved across him.
Jockey Ryan Moore was toiling on the Sir Michael Stoute-trained Estimate from a long way out and eased the filly up near the line.
It was a far cry from June 2013, when the horse won the Gold Cup at the course, the first time that race had been won by a reigning monarch.
The Queen's racing and bloodstock advisor, John Warren, said: "You cannot take the good things away. I think Estimate gave The Queen the biggest thrill she probably ever had in racing.
"The long and short of it is Estimate is now off to stud."
Estimate finished runner-up to Leading Light in this year's Gold Cup but was disqualified from the June contest after testing positive for morphine, which was attributed to innocently contaminated feed.
Ireland took the second race too with the admirable Gordon Lord Byron claiming the Champion Sprint Stakes under Wayne Lordan.
Trainer Tom Hogan said it was a "fairytale" victory for the globetrotting horse whose next stop is likely to be Hong Kong in December,
Charm Spirit scored for France in the Queen Elizabeth II Stakes as runner-up Night Of Thunder, ridden by Richard Hughes, struggled for room and could not catch the victor.
While Hughes switched the 2000 Guineas winner in an attempt to find a gap, Olivier Peslier kept his mount on a straight path to secure victory for trainer Freddie Head.
Meanwhile after Madame Chiang took the Fillies and Mares Stakes for David Simcock, jockey Jim Crowley revealed it was the first time he had sat on the horse.
"So I didn't really know what was under the bonnet. But I'd watched all her races and David had told me all about her and gave very good instructions," said Crowley.
|Champions Day winners|
|Long Distance Cup - Forgotten Rules 3-1 (Dermot Weld/Pat Smullen)|
|Sprint Stakes - Gordon Lord Byron 5-1 joint fav (Tom Hogan/Wayne Lordan)|
|Fillies & Mares Stakes - Madame Chiang 12-1 (David Simcock/Jim Crowley)|
|Queen Elizabeth II Stakes - Charm Spirit 5-1 (Freddie Head/Olivier Peslier)|
|Champion Stakes - Noble Mission 7-1 (Lady Cecil/James Doyle)|
|Balmoral Handicap - Bronze Angel 20-1 (Marcus Tregoning/Louis Steward)|